Fastb

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The fastb file format is a compressed binary form of the fasta format for reads and contigs. (The 'b' in fastb stands for 'binary'.) In fastb, each of the four bases is denoted by two bits -- 00, 01, 10, and 11 -- so that every byte can contain four bases, as in a basevector. Files in this format include reads.fastb and mergedcontigs.fastb.

In Arachne, fastb files are converted into vecbasevector objects for use in modules.

The module FastbStats gives statistics about fastb files, including total, average, and N50 sequence length.


Fastb
Function Conversion
Phase Conversion
Standard CLAs PRE
Special CLAs FILE, FASTAMB
Source location ARACHNE_DIR/util

Module

Fastb is also the name of an executable module. It converts a file from fasta into fastb format. Note that the fastb format cannot store as much information as fasta; in particular, the letter N, representing gaps, has no parallel. When Fastb is run on a fasta file, Ns are converted to random bases, and (if FASTAMB=True) a fastamb file is created that contains the information that was lost.

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